Changes between Version 24 and Version 25 of SOPs/miningSAMBAM

Timestamp:

12/18/14 15:52:12 (10 years ago)

Author:

byuan

Comment:

--

SOPs/miningSAMBAM

@@ -200 +200 @@
 === Split reads by pair ===
 {{{
-# input:        accepted_hits_posStrand.bam or accepted_hits_negStrand.bam
-# output:       1st pair: *_1stPair.bam
-#               2nd pair: *_2ndPair.bam
-bsub "samtools view -b -f 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_1stPair.bam"
-bsub "samtools view -b -F 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_2ndPair.bam"
-bsub "samtools view -b -f 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_1stPair.bam"
-bsub "samtools view -b -F 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_2ndPair.bam"
-}}}
+# input:        accepted_hits.bam
+# output:       1st pair: accepted_hits_1stPair.bam
+#               2nd pair: accepted_hits_2ndPair.bam
+bsub "samtools view -b -f 0x0040 accepted_hits.bam > accepted_hits_1stPair.bam"
+bsub "samtools view -b -F 0x0040 accepted_hits.bam > accepted_hits_2ndPair.bam"
+}}}